g_dyndom(1) [debian man page]
g_dyndom(1) GROMACS suite, VERSION 4.5.4-dev-20110404-bc5695c g_dyndom(1) NAME
g_dyndom - interpolate and extrapolate structure rotations VERSION 4.5.4-dev-20110404-bc5695c SYNOPSIS
g_dyndom -f dyndom.pdb -o rotated.xtc -n domains.ndx -[no]h -[no]version -nice int -firstangle real -lastangle real -nframe int -maxangle real -trans real -head vector -tail vector DESCRIPTION
g_dyndom reads a .pdb file output from DynDom (http://www.cmp.uea.ac.uk/dyndom/). It reads the coordinates, the coordinates of the rota- tion axis, and an index file containing the domains. Furthermore, it takes the first and last atom of the arrow file as command line argu- ments (head and tail) and finally it takes the translation vector (given in DynDom info file) and the angle of rotation (also as command line arguments). If the angle determined by DynDom is given, one should be able to recover the second structure used for generating the DynDom output. Because of limited numerical accuracy this should be verified by computing an all-atom RMSD (using g_confrms) rather than by file comparison (using diff). The purpose of this program is to interpolate and extrapolate the rotation as found by DynDom. As a result unphysical structures with long or short bonds, or overlapping atoms may be produced. Visual inspection, and energy minimization may be necessary to validate the struc- ture. FILES
-f dyndom.pdb Input Protein data bank file -o rotated.xtc Output Trajectory: xtc trr trj gro g96 pdb -n domains.ndx Input Index file OTHER OPTIONS
-[no]hno Print help info and quit -[no]versionno Print version info and quit -nice int 0 Set the nicelevel -firstangle real 0 Angle of rotation about rotation vector -lastangle real 0 Angle of rotation about rotation vector -nframe int 11 Number of steps on the pathway -maxangle real 0 DymDom dtermined angle of rotation about rotation vector -trans real 0 Translation (Angstrom) along rotation vector (see DynDom info file) -head vector 0 0 0 First atom of the arrow vector -tail vector 0 0 0 Last atom of the arrow vector SEE ALSO
gromacs(7) More information about GROMACS is available at <http://www.gromacs.org/>. Mon 4 Apr 2011 g_dyndom(1)
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g_morph(1) GROMACS suite, VERSION 4.5.4-dev-20110404-bc5695c g_morph(1) NAME
g_morph - linear interpolation of conformations VERSION 4.5.4-dev-20110404-bc5695c SYNOPSIS
g_morph -f1 conf1.gro -f2 conf2.gro -o interm.xtc -or rms-interm.xvg -n index.ndx -[no]h -[no]version -nice int -[no]w -xvg enum -ninterm int -first real -last real -[no]fit DESCRIPTION
g_morph does a linear interpolation of conformations in order to create intermediates. Of course these are completely unphysical, but that you may try to justify yourself. Output is in the form of a generic trajectory. The number of intermediates can be controlled with the -ninterm flag. The first and last flag correspond to the way of interpolating: 0 corresponds to input structure 1 while 1 corresponds to input structure 2. If you specify -first 0 or -last 1 extrapolation will be on the path from input structure x1 to x2. In general, the coordinates of the intermediate x(i) out of N total intermidates correspond to: x(i) = x1 + (first+(i/(N-1))*(last-first))*(x2-x1) Finally the RMSD with respect to both input structures can be computed if explicitly selected ( -or option). In that case, an index file may be read to select the group from which the RMS is computed. FILES
-f1 conf1.gro Input Structure file: gro g96 pdb tpr etc. -f2 conf2.gro Input Structure file: gro g96 pdb tpr etc. -o interm.xtc Output Trajectory: xtc trr trj gro g96 pdb cpt -or rms-interm.xvg Output, Opt. xvgr/xmgr file -n index.ndx Input, Opt. Index file OTHER OPTIONS
-[no]hno Print help info and quit -[no]versionno Print version info and quit -nice int 0 Set the nicelevel -[no]wno View output .xvg, .xpm, .eps and .pdb files -xvg enum xmgrace xvg plot formatting: xmgrace, xmgr or none -ninterm int 11 Number of intermediates -first real 0 Corresponds to first generated structure (0 is input x0, see above) -last real 1 Corresponds to last generated structure (1 is input x1, see above) -[no]fityes Do a least squares fit of the second to the first structure before interpolating SEE ALSO
gromacs(7) More information about GROMACS is available at <http://www.gromacs.org/>. Mon 4 Apr 2011 g_morph(1)